BA 1984, Harvard University PhD 1989, UC Berkeley Honors 2024 Nobel Prize in Chemistry 2023 Frontiers of Knowledge Award in Biology and Biomedicine 2021 The Breakthrough Prize, Life Sciences 2020 – Fellow, American Institute for Medical and Biological Engineering 2019 The Audacious Project Recipient 2018 Protein Society Hans Neurath Award 2018 Solvay Public Lecture 2017 – Henrietta and Aubrey Davis Endowed Professorship in Biochemistry 2014 American Chemical Society David Perlman Memorial Award 2012 Biochemical Society Centenary Award 2011 University of Washington Inventor of the Year Award 2009 – American Academy of Sciences 2008 Sackler Prize in Biophysics 2006 – National Academy of Sciences 2005 – HHMI Investigator 2004 Foresight Institute Feynman Prize 2004 AAAS Newcomb–Cleveland Prize 2003 – 2004 Director, Biomolecular Structure and Design Graduate Program (BMSD) 2002 International Society for Computational Biology Overton Prize 2000 Protein Society Young Investigator Award 2000 – 2005 HHMI Associate Investigator 1995 Beckman Young Investigator Award 1994 Packard Fellowship in Science and Engineering 1994 National Science Foundation Young Investigator Award

Our research is focused on the prediction and design of protein structures, protein folding mechanisms, protein-protein interactions, protein-nucleotide interactions, and protein-ligand interactions. Our approach is to use experiments to understand the fundamental principles underlying these problems, to develop simple computational models based on these insights, and to test the models through structure prediction and design. We strive to continually improve our methodology by iterating between computational and experimental studies.

Li Y, Harris BS, Li Z, Shi C, Abdullah J, Majumder S, Berhanu S, Vorobieva AA, Myers SK, Hettige J, Baer MD, De Yoreo JJ, Baker D, Noy A. Water, Solute, and Ion Transport in De Novo-Designed Membrane Protein Channels. ACS Nano 2024 Dec; [PMID:39714958] King BR, Sumida KH, Caruso JL, Baker D, Zalatan JG. Computational Stabilization of a Non-Heme Iron Enzyme Enables Efficient Evolution of New Function. Angew Chem Int Ed Engl 2024 Oct; [PMID:39394803] Jin B, Chen Y, Pyles H, Baer MD, Legg BA, Wang Z, Washton NM, Mueller KT, Baker D, Schenter GK, Mundy CJ, De Yoreo JJ. Formation, chemical evolution and solidification of the dense liquid phase of calcium (bi)carbonate. Nat Mater 2024 Oct; [PMID:39448841] [PMCID:8906573] Zhang JZ, Ong SE, Baker D, Maly DJ. Single-cell sensor analyses reveal signaling programs enabling Ras-G12C drug resistance. Nat Chem Biol 2024 Aug; [PMID:39103633] [PMCID:3531194] Kibler RD, Lee S, Kennedy MA, Wicky BIM, Lai SM, Kostelic MM, Carr A, Li X, Chow CM, Nguyen TK, Carter L, Wysocki VH, Stoddard BL, Baker D. Design of pseudosymmetric protein hetero-oligomers. Nat Commun 2024 Dec; 15(1):10684. [PMID:39695145] [PMCID:PMC11655659] Glögl M, Krishnakumar A, Ragotte RJ, Goreshnik I, Coventry B, Bera AK, Kang A, Joyce E, Ahn G, Huang B, Yang W, Chen W, Sanchez MG, Koepnick B, Baker D. Target-conditioned diffusion generates potent TNFR superfamily antagonists and agonists. Science 2024 Dec; 386(6726):1154-1161. [PMID:39636970] Sun K, Li S, Zheng B, Zhu Y, Wang T, Liang M, Yao Y, Zhang K, Zhang J, Li H, Han D, Zheng J, Coventry B, Cao L, Baker D, Liu L, Lu P. Accurate de novo design of heterochiral protein-protein interactions. Cell Res 2024 Dec; 34(12):846-858. [PMID:39143121] [PMCID:PMC2815670] Zhang JZ, Nguyen WH, Greenwood N, Rose JC, Ong SE, Maly DJ, Baker D. Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution. Nat Biotechnol 2024 Dec; 42(12):1888-1898. [PMID:38273065] [PMCID:PMC11631767] Baryshev A, La Fleur A, Groves B, Michel C, Baker D, Ljubetič A, Seelig G. Massively parallel measurement of protein-protein interactions by sequencing using MP3-seq. Nat Chem Biol 2024 Nov; 20(11):1514-1523. [PMID:39192093] [PMCID:PMC5568797] Humphreys IR, Zhang J, Baek M, Wang Y, Krishnakumar A, Pei J, Anishchenko I, Tower CA, Jackson BA, Warrier T, Hung DT, Peterson SB, Mougous JD, Cong Q, Baker D. Protein interactions in human pathogens revealed through deep learning. Nat Microbiol 2024 Oct; 9(10):2642-2652. [PMID:39294458] [PMCID:PMC9992841] Moyer AP, Ramelot TA, Curti M, Eastman MA, Kang A, Bera AK, Tejero R, Salveson PJ, Curutchet C, Romero E, Montelione GT, Baker D. Enumerative Discovery of Noncanonical Polypeptide Secondary Structures. J Am Chem Soc 2024 Sep; 146(37):25501-25512. [PMID:39231524] [PMCID:PMC4393527] Yang EC, Divine R, Miranda MC, Borst AJ, Sheffler W, Zhang JZ, Decarreau J, Saragovi A, Abedi M, Goldbach N, Ahlrichs M, Dobbins C, Hand A, Cheng S, Lamb M, Levine PM, Chan S, Skotheim R, Fallas J, Ueda G, Lubner J, Somiya M, Khmelinskaia A, King NP, Baker D. Computational design of non-porous pH-responsive antibody nanoparticles. Nat Struct Mol Biol 2024 Sep; 31(9):1404-1412. [PMID:38724718] [PMCID:PMC3855844] Huang B, Coventry B, Borowska MT, Arhontoulis DC, Exposit M, Abedi M, Jude KM, Halabiya SF, Allen A, Cordray C, Goreshnik I, Ahlrichs M, Chan S, Tunggal H, DeWitt M, Hyams N, Carter L, Stewart L, Fuller DH, Mei Y, Garcia KC, Baker D. De novo design of miniprotein antagonists of cytokine storm inducers. Nat Commun 2024 Aug; 15(1):7064. [PMID:39152100] [PMCID:PMC7422941] Berger S, Seeger F, Yu TY, Aydin M, Yang H, Rosenblum D, Guenin-Macé L, Glassman C, Arguinchona L, Sniezek C, Blackstone A, Carter L, Ravichandran R, Ahlrichs M, Murphy M, Pultz IS, Kang A, Bera AK, Stewart L, Garcia KC, Naik S, Spangler JB, Beigel F, Siebeck M, Gropp R, Baker D. Preclinical proof of principle for orally delivered Th17 antagonist miniproteins. Cell 2024 Aug; 187(16):4305-4317.e18. [PMID:38936360] [PMCID:PMC10418464] Pillai A, Idris A, Philomin A, Weidle C, Skotheim R, Leung PJY, Broerman A, Demakis C, Borst AJ, Praetorius F, Baker D. De novo design of allosterically switchable protein assemblies. Nature 2024 Aug; 632(8026):911-920. [PMID:39143214] [PMCID:PMC5734394] Jiang H, Jude KM, Wu K, Fallas J, Ueda G, Brunette TJ, Hicks DR, Pyles H, Yang A, Carter L, Lamb M, Li X, Levine PM, Stewart L, Garcia KC, Baker D. De novo design of buttressed loops for sculpting protein functions. Nat Chem Biol 2024 Aug; 20(8):974-980. [PMID:38816644] [PMCID:PMC11288887] Sahtoe DD, Andrzejewska EA, Han HL, Rennella E, Schneider MM, Meisl G, Ahlrichs M, Decarreau J, Nguyen H, Kang A, Levine P, Lamb M, Li X, Bera AK, Kay LE, Knowles TPJ, Baker D. Design of amyloidogenic peptide traps. Nat Chem Biol 2024 Aug; 20(8):981-990. [PMID:38503834] [PMCID:PMC5734394] Berhanu S, Majumder S, Müntener T, Whitehouse J, Berner C, Bera AK, Kang A, Liang B, Khan N, Sankaran B, Tamm LK, Brockwell DJ, Hiller S, Radford SE, Baker D, Vorobieva AA. Sculpting conducting nanopore size and shape through de novo protein design. Science 2024 Jul; 385(6706):282-288. [PMID:39024453] [PMCID:PMC10885333] An L, Said M, Tran L, Majumder S, Goreshnik I, Lee GR, Juergens D, Dauparas J, Anishchenko I, Coventry B, Bera AK, Kang A, Levine PM, Alvarez V, Pillai A, Norn C, Feldman D, Zorine D, Hicks DR, Li X, Sanchez MG, Vafeados DK, Salveson PJ, Vorobieva AA, Baker D. Binding and sensing diverse small molecules using shape-complementary pseudocycles. Science 2024 Jul; 385(6706):276-282. [PMID:39024436] [PMCID:PMC11542606] Edman NI, Phal A, Redler RL, Schlichthaerle T, Srivatsan SR, Ehnes DD, Etemadi A, An SJ, Favor A, Li Z, Praetorius F, Gordon M, Vincent T, Marchiano S, Blakely L, Lin C, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray A, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Zheng Y, Murry CE, Schweppe DK, Freedman BS, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. Cell 2024 Jul; 187(14):3726-3740.e43. [PMID:38861993] [PMCID:PMC7295121] Peruzzi JA, Gunnels TF, Edelstein HI, Lu P, Baker D, Leonard JN, Kamat NP. Enhancing extracellular vesicle cargo loading and functional delivery by engineering protein-lipid interactions. Nat Commun 2024 Jul; 15(1):5618. [PMID:38965227] [PMCID:PMC3855844] Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S, Choudhury J, Dauparas J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, Correia BE. Computational design of soluble and functional membrane protein analogues. Nature 2024 Jul; 631(8020):449-458. [PMID:38898281] [PMCID:PMC6608625] Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V, Shareef S, Sica AV, Hua AS, Deshmukh AP, Moyer AP, Hicks DR, Swartz AZ, Cacho RA, Novy N, Bera AK, Kang A, Sankaran B, Johnson MP, Phadkule A, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram JR, Stoddard BL, Romero E, Hunter CN, Baker D. De novo design of proteins housing excitonically coupled chlorophyll special pairs. Nat Chem Biol 2024 Jul; 20(7):906-915. [PMID:38831036] [PMCID:PMC3359726] Shen H, Lynch EM, Akkineni S, Watson JL, Decarreau J, Bethel NP, Benna I, Sheffler W, Farrell D, DiMaio F, Derivery E, De Yoreo JJ, Kollman J, Baker D. De novo design of pH-responsive self-assembling helical protein filaments. Nat Nanotechnol 2024 Jul; 19(7):1016-1021. [PMID:38570702] [PMCID:PMC6029841] Peruzzi JA, Steinkühler J, Vu TQ, Gunnels TF, Hu VT, Lu P, Baker D, Kamat NP. Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes. Nat Commun 2024 Apr; 15(1):3162. [PMID:38605024] [PMCID:PMC6901749]